forked from pool/bcftools
b90d9d1f57
- Update to version 1.19 Too many changes to list, for details see https://github.com/samtools/bcftools/releases/tag/1.19 - Update to version 1.18 Too many changes to list, for details see https://github.com/samtools/bcftools/releases/tag/1.18 - Update to version 1.17 Too many changes to list, for details see https://github.com/samtools/bcftools/releases/tag/1.17 OBS-URL: https://build.opensuse.org/request/show/1136376 OBS-URL: https://build.opensuse.org/package/show/science/bcftools?expand=0&rev=19
66 lines
2.5 KiB
Diff
66 lines
2.5 KiB
Diff
From: toddrme2178@gmail.com
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Date: 2020-02-12
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Subject: Use python3 instead of python2
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The package currently uses the "python" executable, but it should be
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python3 compatible according to the documentation. This patch changes
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all the executables to use "python3" instead of "python".
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diff -Nur bcftools-1.15.1/doc/bcftools.1 new/doc/bcftools.1
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--- bcftools-1.15.1/doc/bcftools.1 2022-04-07 17:32:58.000000000 +0200
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+++ new/doc/bcftools.1 2022-04-21 17:54:28.011999739 +0200
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@@ -5841,7 +5841,7 @@
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.fam C
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# The final looks can be customized by editing the generated
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# \*(Aqoutdir/plot.py\*(Aq script and re\-running manually
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-cd outdir && python plot.py && pdflatex summary.tex
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+cd outdir && python3 plot.py && pdflatex summary.tex
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.fam
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.fi
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.if n .RE
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diff -Nur bcftools-1.15.1/doc/bcftools.html new/doc/bcftools.html
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--- bcftools-1.15.1/doc/bcftools.html 2022-04-07 17:32:58.000000000 +0200
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+++ new/doc/bcftools.html 2022-04-21 17:54:28.011999739 +0200
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@@ -4942,7 +4942,7 @@
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<div class="content">
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<pre># The final looks can be customized by editing the generated
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# 'outdir/plot.py' script and re-running manually
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-cd outdir && python plot.py && pdflatex summary.tex</pre>
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+cd outdir && python3 plot.py && pdflatex summary.tex</pre>
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</div>
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</div>
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</div>
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diff -Nur bcftools-1.15.1/doc/bcftools.txt new/doc/bcftools.txt
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--- bcftools-1.15.1/doc/bcftools.txt 2022-03-03 16:10:50.000000000 +0100
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+++ new/doc/bcftools.txt 2022-04-21 17:54:28.011999739 +0200
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@@ -3635,7 +3635,7 @@
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# The final looks can be customized by editing the generated
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# 'outdir/plot.py' script and re-running manually
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- cd outdir && python plot.py && pdflatex summary.tex
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+ cd outdir && python3 plot.py && pdflatex summary.tex
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--
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diff -Nur bcftools-1.15.1/misc/guess-ploidy.py new/misc/guess-ploidy.py
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--- bcftools-1.15.1/misc/guess-ploidy.py 2021-06-23 12:49:05.000000000 +0200
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+++ new/misc/guess-ploidy.py 2022-04-21 17:53:16.863999747 +0200
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@@ -1,4 +1,4 @@
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-#!/usr/bin/env python
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+#!/usr/bin/env python3
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#
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# Plot the output of "bcftools +guess-ploidy -v"
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#
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diff -Nur bcftools-1.15.1/vcfcnv.c new/vcfcnv.c
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--- bcftools-1.15.1/vcfcnv.c 2022-02-17 13:45:09.000000000 +0100
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+++ new/vcfcnv.c 2022-04-21 17:53:54.239999743 +0200
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@@ -321,7 +321,7 @@
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{
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if ( th>100 ) return; // create no plots
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- char *cmd = msprintf("python %s -p %f", script, th);
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+ char *cmd = msprintf("python3 %s -p %f", script, th);
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int ret = system(cmd);
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if ( ret) fprintf(stderr, "The command returned non-zero status %d: %s\n", ret, cmd);
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free(cmd);
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